/* 
 * File:   BamReader.h
 * Author: hyjkim
 *
 * Utilizes samtools api in order to read a bam file
 * and send a group of related reads to HLATree to generate
 * a read tree.
 *
 * Created on April 26, 2012, 2:44 PM
 */


#include <string>
#include <iostream>
#include <sstream>
#include "sam.h"

#define MISMATCH 0
#define INSERTION 1
#define DELETION 2

class BamReader {

    public:
    void respond ();
    void openBam(std::string filename);
    void testOpenBam(std::string filename);

};

class variant {
    int _start;
    int _end;
    uint8_t _type;
    std::string _variant;
    public:
    variant(uint8_t type) {
        _type = type;
    }
    void setStart(int start) {
        _start = start;
    }
    void setEnd(int end) {
        _end = end;
    }
    void setVariant (std::string variant) {
        _variant = variant;
    }
};
